*2.1. Screening Procedures*

The selected patients underwent an infectious screening (HBsAg, HBcAb, HBsAb; HCV-Ab; quantiferon-TB gold assay, chest X-ray, HIV-Ab, HPV test, VZV-Ab, EBV-Ab) before starting adalimumab therapy. Clinical history, data on physical examination, instrumental examinations, recent biochemical examinations and signed informed consent for the purpose of enrolment in the study were collected. Before starting adalimumab therapy, a faecal sample from the patients was taken, collected in the previous 24 h, in a sterile container, with the caution to reduce as much as possible contaminating contacts of the sample. The faecal samples were associated with a numerical identification code and stored frozen at −80 ◦C. Two faecal samples were collected from each CD patient; the first before the start of adalimumab therapy and the second after six months of treatment. The samples underwent metagenomic NGS (next generation sequencing or sequencing in parallel) sequencing with the use of the Illumina MiSeq platform (San Diego, CA, USA) following the amplification of the V3-V4 regions of the 16s-rRNA gene (ribosomal 16-S gene) using a 2 × 300 bp-end approach [9–11].
